ClearBooks vs Puzzle: which AI accounting software fits your startup?

The short answer

Puzzle is AI-native accounting software that, since its "Puzzle 2.0" release, also sells accounting services on top of the platform. Its AI Suite (Chat, Cowork, and Close) categorizes, reconciles, and drafts financials for you to review, and Puzzle says it automatically categorizes 85–90% of transactions with no rules to write. You can then add Puzzle accountants or a vetted partner firm, from a monthly expert review to a fully managed close (source).

ClearBooks is also software with an AI bookkeeping agent. The agent works through permissioned tools: it categorizes, reconciles, drafts invoices, runs reports, and proposes journal entries, and every change it wants to make is shown to you as a Confirm/Cancel card first. The same books are open to your own agents through an MCP server (300+ tools) and a REST API (280+ endpoints).

The difference is scope. Puzzle goes deeper on the core close (revenue recognition, accruals, subledgers) and sells human services around it. ClearBooks goes wider on what a young C-corp files and tracks: payroll, Form 1120 and California Form 100, and the cap table, all from one ledger.

Feature comparison

Puzzle's services are priced separately and can only be bought with a Puzzle software plan. Check the Puzzle pricing page for current service and add-on prices.

Where Puzzle is better

Be honest about what you are giving up:

• Maturity and scale. Puzzle says 10,000+ companies run on it (source). ClearBooks is a younger product with fewer customers and fewer edge cases behind it.
• Integrations. Puzzle has direct integrations with Stripe, Mercury, Brex, Ramp, Gusto, Rippling, Deel, and Bill.com on top of Plaid (source). ClearBooks' live integrations are a shorter list (Plaid, Brex, Stripe, Zapier, webhooks, CSV).
• Accrual depth. Puzzle offers revenue recognition, accrual and prepaid automation, classes, departments and projects, and subledgers on its higher plans. ClearBooks supports double-entry journal entries and fixed assets, but not automated revenue recognition.
• People when you need them. Puzzle sells monthly bookkeeping review, a fully managed close with a named bookkeeper, catch-up bookkeeping, tax filing through a partner firm, and fractional CFO and controller services on the same platform (source). ClearBooks does not supply bookkeepers; you invite your own.
• Migration help. Puzzle imports QuickBooks history and offers a paid migration service. ClearBooks has no direct QuickBooks import yet.
• Running payroll for you. Puzzle's payroll add-on is a service that runs payroll for you. ClearBooks payroll calculates paychecks and posts them to the ledger, but you move the money and file the returns yourself.

Where ClearBooks is better

• Startup filings from the ledger. ClearBooks prepares Form 1120 (with Schedules C, J, K, L, M-1, M-2) and California Form 100 from your books and fills the official IRS and FTB PDFs for you or your CPA to review and file. Puzzle offers a tax report on every plan and sells tax filing through a partner firm as an add-on. See tax.
• Payroll in the same database as the books. ClearBooks calculates federal withholding, FICA, FUTA, and California, Texas, and Arizona state taxes, posts each approved pay run as a journal entry, and prepares Form 941, 940, W-2, and state wage report figures. It does not do direct deposit or e-file. See payroll.
• Cap table next to the ledger. Track SAFEs with valuation caps and discounts, convertible notes, priced rounds, and option pool reservations, and share investor data rooms by link. See equity.
• Period locks that hold for every caller. Soft and hard closes are enforced by database triggers, so the app, the REST API, the MCP server, and the AI agent are all held to the same lock. See reconciliation and close.
• Scoped access for your own agents. Every MCP tool and API endpoint declares a read or write scope per resource, such as invoices or payroll, so you can give an agent exactly the access it needs. The REST API is self-serve from the Developer Portal on paid plans.
• Price at pre-seed. ClearBooks has a free Starter plan, and the Pro plan, which includes AI categorization and API access, is $29/month.

Switching from Puzzle to ClearBooks

There is no direct Puzzle importer. The practical path:

1. Close your last full month in Puzzle and export the chart of accounts, trial balance, and transaction detail.
2. Import transactions by CSV and enter opening balances as journal entries in ClearBooks.
3. Connect bank and card accounts through Plaid so new activity flows in, and let the agent categorize it.
4. Reconcile the first month against your bank statements before you rely on the reports.

ClearBooks exports journal entries in QuickBooks IIF format and as a Xero manual-journal CSV, so you can move again later. The docs cover imports in detail.

Who should pick which

Pick Puzzle if you want a more established AI accounting platform, you rely on Mercury, Ramp, Gusto, Rippling, or Deel integrations, you need revenue recognition and accrual automation, or you want the option to hand the monthly close, tax filing, or CFO work to accountants without switching tools.

Pick ClearBooks if you are a US C-corp startup that wants an AI agent to do the bookkeeping while you approve each change, you want Form 1120 and California Form 100 drafted from your ledger, you want payroll figures and your SAFEs in the same system as your books, and you want to start free. Compare plans on the pricing page.

Frequently asked questions